High-resolution RNA isoform variation analysis by combining the advantages of single-cell RNA and nanopore sequencing

TY - ABST

T1 - High-resolution RNA isoform variation analysis by combining the advantages of single-cell RNA and nanopore sequencing

AU - Zhou, Xiaoyu

AU - Rahimi, Karim

AU - Kjems, Jørgen

AU - Lin, Lin

PY - 2023

Y1 - 2023

N2 - Endothelial cell (EC) heterogeneity medical research was restricted by limited human sample diversity and in vivo methods, and bulk RNA tissue-level analysis results usually depend on most cell types. The pig is a commonly used biomedical model for human diseases and xenotransplantation due to the close physiological and genetic resemblance and the similarity in the organ size. We combined the advantages of single-cell mRNA barcoding 10X Genomics technology with nanopore long reads sequence to identify novel isoforms and establish the RNA isoform atlas of Sus scrofa domestica. The Spearman’s rank correlation coefficient between the next-generation sequence and cleaned-up full-length cDNA reads each barcode is 0.86 [0.79-0.94]. Statistical tests of the ECs in the brain, adipose, liver and retina to discover hundreds of different transcript usage (DTU) genesets on a pseudo-bulk level. Although more accurate transcriptome quantification, it’s difficult to find tissue-specific gene markers of endothelial cells in subcutaneous adipose and visceral adipose, compared with T cells and macrophages. Adiposes are also peripheral organs with the nervous system and immune cells. There are distinguish DTU genesets among different adipocyte functions. Several cell surface marker genes present highly heterogeneous DTU across different cell types.

AB - Endothelial cell (EC) heterogeneity medical research was restricted by limited human sample diversity and in vivo methods, and bulk RNA tissue-level analysis results usually depend on most cell types. The pig is a commonly used biomedical model for human diseases and xenotransplantation due to the close physiological and genetic resemblance and the similarity in the organ size. We combined the advantages of single-cell mRNA barcoding 10X Genomics technology with nanopore long reads sequence to identify novel isoforms and establish the RNA isoform atlas of Sus scrofa domestica. The Spearman’s rank correlation coefficient between the next-generation sequence and cleaned-up full-length cDNA reads each barcode is 0.86 [0.79-0.94]. Statistical tests of the ECs in the brain, adipose, liver and retina to discover hundreds of different transcript usage (DTU) genesets on a pseudo-bulk level. Although more accurate transcriptome quantification, it’s difficult to find tissue-specific gene markers of endothelial cells in subcutaneous adipose and visceral adipose, compared with T cells and macrophages. Adiposes are also peripheral organs with the nervous system and immune cells. There are distinguish DTU genesets among different adipocyte functions. Several cell surface marker genes present highly heterogeneous DTU across different cell types.

M3 - Conference abstract for conference

SP - 44

T2 - Neuroscience Day

Y2 - 13 June 2023 through 13 June 2023

ER -